Medicago truncatula vs Cucumis sativus LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Cucumis sativus (Cucumis sativus, ASM407v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Medicago truncatula was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 156,335

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula

Uncovered: 362,862,129 out of 412,800,391
Covered: 49,938,262 out of 412,800,391

Uncovered: 18,236,094 out of 50,132,764
Matches: 21,794,099 out of 50,132,764
Mismatches: 9,428,167 out of 50,132,764
Insertions: 674,404 out of 50,132,764

Cucumis sativus

Uncovered: 157,525,709 out of 193,829,320
Covered: 36,303,611 out of 193,829,320

Uncovered: 4,530,056 out of 26,192,424
Matches: 14,859,146 out of 26,192,424
Mismatches: 6,286,984 out of 26,192,424
Insertions: 516,238 out of 26,192,424

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Medicago truncatula Cucumis sativus
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}